Sai Kumar Ramadugu wrote:
Dear All,
I'm running set of umbrella sampling simulations to get the PMF of a
disaccharide binding to a protein.
I followed the tutorial provided by Justin and changed the values of
necessary parameters according to my system.
The mdp file for umbrella sampling simulations is as follows:
---
; Pull code
pull= umbrella
pull_geometry = distance ; can't get PMF with direction
pull_dim= N N Y
pull_start = yes
pull_ngroups= 1
pull_group0 = active_site
pull_pbcatom0 = 575
pull_group1 = new
pull_pbcatom1 = 1500
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 750 ; kJ mol^-1 nm^-2
pull_nstxout= 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
Active site in the pull_group0 being the residues in the binding site
and new in the pull_group1 being the disaccharide.
Initially I did an SMD run where I separated the disaccharide from the
binding upto 1.5nm in distance.
When I started running the umbrella sampling simulations, I used the
conformations with approximately 0.1nm difference starting from an
initial separation of 0.3nm between the binding site residues and
disaccharide.
My question is: when I run g_wham and get the profile, the pmf reaches a
plateau, but its not completely horizontal. It drops down a little. Is
it acceptable to have the pmf reach a plateau but not completely horizontal?
It looks like you just have a very rocky PMF, indicating that you probably
haven't sampled sufficiently (i.e., the simulations are probably too short).
In the histogram, the first two windows have good overlap and are narrow
distributions where as the later windows are spread out.
I have tried to decrease the distance from 0.1 nm to 0.05 nm and still
the sampling around 0.5-0.75 of Xi region does not sample well.
Is there anything that you could suggest?
More windows and/or longer simulations.
-Justin
I have uploaded the plots of profile and histograms.
PMF Plot link: http://img801.imageshack.us/i/pmf.png/
Histogram link: http://img217.imageshack.us/i/histoy.png/
Thanks for your time
Sai Ramadugu
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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